In my opinion, there is a difference between conceptual learning and muscle memory training. In addition, different people have different learning styles. A kinetic learner will study concepts in a different manner than an auditory learner. The nature of the instrument we study colors our understanding of music and music theory.
I'm a drummer, so my approach to studying a piece of music is to hear it in pattern layers. Even the most complex arrangements can be simplified by breaking them down and examining each layer individually. Hearing the patterns, I can follow each line and how they interact with one another. When I write a song, I "hear" each layer in my mind before playing a single note. Obviously, others take a different approach.
In high school, I started picking out notes on a piano in an attempt to explain parts to other musicians. A pianist took pity on me and taught me a small amount of theory. Armed with an insignificant amount of knowledge, I wrote some songs. The pianist was fascinated. "How can you write music with absolutely no idea what you are doing?" he asked. I could only say that I tried to play the notes and chords I heard in my head. He watched, fascinated, as I slammed the keyboard. He would interrupt occasionally to tell me that some of my chord combinations should not have worked, but he thought they sounded great. He explained to me that as a pianist, he thought of music in a certain way and it colored his concepts. He also told me to stop hitting the keyboard so hard. I had a lot to learn.
I've known musicians who lacked the music theory education to articulate their musical ideas. I've also known musicians whose vast understanding of theory was not matched with their muscle memory. For some, playing music is a mental/emotional exercise and the muscle memory technique is merely a tool for the job. Others I've known enjoy the mastery of the technique more than the conceptual comprehension. I can see that there is a certain degree of pleasure in both.
When I'm learning concepts, I can't follow abstract discussions of music theory, but I can appreciate explanation coupled with demonstration. When I'm studying muscle memory, I need it broken down in to simple pieces. As I master each one at a slow speed, I can put them together and speed it up. I've always believed as a drummer that if I can think of the part, I can play it. To me, conceptualizing the layers of the drum part is essential to playing it. When I'm playing, I'm listening to the layers; how the drum part interacts with the bass, guitar, keys and vocals. Everything I'm playing shifts to the background, because I've already thought it through, and I'm thinking about what's coming next. I'm listening for that build into the chorus, the drive into the bridge, opening up space in the verse, etc. On the way, I'll sometimes imagine some fills that will fit where the song is going. As I think of them, they are added to the overall pattern, and then I play them. I never thought about which stick I would lead with, the mechanics of the fill, or even counting the time. Instead, I thought about the feel of the song, leading the vocal to the climax of the chorus, snapping into the rhythm guitar's hook, nailing that downbeat with the bass, etc.
That's just me, though. YMMV.